* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2015-11-24 19:35 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-11-24 19:35 UTC (permalink / raw
To: gentoo-commits
commit: e7b6d94becba4bcca6255dbcee732b53f9c41e02
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 24 19:34:44 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 24 19:34:44 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e7b6d94b
sci-biology/repeatmasker: improve einfo message
Package-Manager: portage-2.2.18
sci-biology/repeatmasker/ChangeLog | 4 ++++
sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild | 3 ++-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index 67ed4e6..c7fadb6 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ repeatmasker-4.0.1-r1.ebuild:
+ sci-biology/repeatmasker: improve einfo message
+
*repeatmasker-4.0.1-r1 (24 Nov 2015)
24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
index 9507e23..0899978 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
@@ -91,7 +91,8 @@ pkg_postinst(){
einfo "RepeatMasker provides bundled human repeats database"
einfo "from Dfam-1.0 database www.dfam.org"
einfo "You can configure which search search engine is to be used and"
- einfo "PATHs to the search binaries in RepeatMaskerConfig.pm"
+ einfo "PATHs to the search binaries are defined in"
+ einfo "/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
einfo "Supported search engines are:"
einfo "cross_match from sci-biology/phrap"
einfo "rmblast from sci-biology/rmblast"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2015-12-06 19:37 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-12-06 19:37 UTC (permalink / raw
To: gentoo-commits
commit: 89c3d525fd3f87807f0233a6a561da7873a559f9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec 6 19:37:00 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec 6 19:37:00 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89c3d525
sci-biology/repeatmasker: fix ebuild so that it installs files in a proper location
Package-Manager: portage-2.2.26
sci-biology/repeatmasker/ChangeLog | 7 +++++++
.../{repeatmasker-4.0.6.ebuild => repeatmasker-4.0.6-r1.ebuild} | 9 ++++++---
2 files changed, 13 insertions(+), 3 deletions(-)
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index 872aa83..86d8a7a 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*repeatmasker-4.0.6-r1 (06 Dec 2015)
+
+ 06 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +repeatmasker-4.0.6-r1.ebuild, -repeatmasker-4.0.6.ebuild:
+ sci-biology/repeatmasker: fix ebuild so that it installs files in a proper
+ location
+
01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+files/repeatmasker-4.0.6__configure.patch,
-files/RepeatMasker-open-4-0-1__configure.patch,
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild
similarity index 91%
rename from sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
rename to sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild
index 89b7c7f..c7f93fb 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild
@@ -58,7 +58,7 @@ Y
Y
5" | "${S}/configure" || die "configure failed"
sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
- -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
+ -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/Libraries/\1"|' \
-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
}
@@ -74,14 +74,17 @@ src_install() {
dodir /usr/share/${PN}/lib
insinto /usr/share/${PN}/lib
- doins "${S}"/*.pm || die
+ doins "${S}"/*.pm
+ insinto /usr/share/${PN}/lib/Libraries
+ doins "${S}"/Libraries/*.pm
+ rm -rf "${S}"/Libraries/*.pm # zap the supposedly misplaced RepeatAnnotationData.pm file
# if sci-biology/repeatmasker-libraries is installed prevent file collision
# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
# a limited version of the file: 20110419-min
rm -rf Libraries/RepeatMaskerLib.embl
insinto /usr/share/${PN}
- doins -r util Matrices Libraries taxonomy.dat *.help || die
+ doins -r util Matrices Libraries *.help
keepdir /usr/share/${PN}/Libraries
dodoc README INSTALL *.help
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2015-12-06 19:49 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-12-06 19:49 UTC (permalink / raw
To: gentoo-commits
commit: 69f643034bc683d3e26f4d5185d09a91e2975667
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec 6 19:48:34 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec 6 19:48:34 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=69f64303
sci-biology/repeatmasker: actually the the utilities do not include Libraries/ in the paths so install it along all other *.pm files
Package-Manager: portage-2.2.26
sci-biology/repeatmasker/ChangeLog | 7 +++++++
.../{repeatmasker-4.0.6-r1.ebuild => repeatmasker-4.0.6-r2.ebuild} | 4 +---
2 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index 86d8a7a..0c329e5 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*repeatmasker-4.0.6-r2 (06 Dec 2015)
+
+ 06 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +repeatmasker-4.0.6-r2.ebuild, -repeatmasker-4.0.6-r1.ebuild:
+ sci-biology/repeatmasker: actually the the utilities do not include Libraries/
+ in the paths so install it along all other *.pm files
+
*repeatmasker-4.0.6-r1 (06 Dec 2015)
06 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
similarity index 97%
rename from sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild
rename to sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
index c7f93fb..86be5af 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r1.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
@@ -74,9 +74,7 @@ src_install() {
dodir /usr/share/${PN}/lib
insinto /usr/share/${PN}/lib
- doins "${S}"/*.pm
- insinto /usr/share/${PN}/lib/Libraries
- doins "${S}"/Libraries/*.pm
+ doins "${S}"/*.pm "${S}"/Libraries/*.pm
rm -rf "${S}"/Libraries/*.pm # zap the supposedly misplaced RepeatAnnotationData.pm file
# if sci-biology/repeatmasker-libraries is installed prevent file collision
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2016-04-12 16:03 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2016-04-12 16:03 UTC (permalink / raw
To: gentoo-commits
commit: 80c51e8b364ef855d6406f6db9ab304de7705079
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 12 16:00:08 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 12 16:00:08 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=80c51e8b
sci-biology/repeatmasker: add DEPENDency on dev-perl/Text-Soundex as it now landed the main repo (was bug #566740)
Package-Manager: portage-2.2.28
sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
index 18e3e69..7a64c7e 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -22,8 +22,8 @@ RDEPEND="
sci-biology/rmblast
>=sci-biology/trf-4.0.4
sci-biology/repeatmasker-libraries
- sci-biology/phrap"
-# dev-perl/Text-Soundex see bug #566740
+ sci-biology/phrap
+ dev-perl/Text-Soundex"
S="${WORKDIR}/RepeatMasker"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-10 1:03 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-10 1:03 UTC (permalink / raw
To: gentoo-commits
commit: b0969f05ac32a1bf417d7438ad47ab7ceae9e9ec
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:02:20 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:02:20 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0969f05
sci-biology/repeatmasker: improve installation process
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...peatmasker-4.0.6-r2.ebuild => repeatmasker-4.0.6-r3.ebuild} | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
similarity index 94%
rename from sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
rename to sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 7a64c7e..c320942 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -72,16 +72,16 @@ src_install() {
dosym /usr/share/${PN}/$i /usr/bin/$i
done
- dodir /usr/share/${PN}/lib
- insinto /usr/share/${PN}/lib
+ perl_set_version
+ insinto "${VENDOR_LIB}"
doins "${S}"/*.pm "${S}"/Libraries/*.pm
# zap the supposedly misplaced RepeatAnnotationData.pm file
- rm -rf "${S}"/Libraries/*.pm || die
+ rm -r "${S}"/Libraries/*.pm || die
# if sci-biology/repeatmasker-libraries is installed prevent file collision
# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
# a limited version of the file: 20110419-min
- rm -rf Libraries/RepeatMaskerLib.embl || die
+ rm -r Libraries/RepeatMaskerLib.embl || die
insinto /usr/share/${PN}
doins -r util Matrices Libraries *.help
keepdir /usr/share/${PN}/Libraries
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-29 11:59 Justin Lecher
0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2017-01-29 11:59 UTC (permalink / raw
To: gentoo-commits
commit: e9643bc810aa1b949e80bc0619831f7235c5b9e4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 11:46:31 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 11:59:23 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9643bc8
sci-biology/repeatmasker: QA fixes
BUMP EAPI to 6
sort deps
use optfeature
Add missing quotes
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index c320942..3da4241 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit eutils
@@ -19,11 +19,12 @@ IUSE=""
DEPEND=">=dev-lang/perl-5.8"
RDEPEND="
+ dev-perl/Text-Soundex
+ sci-biology/phrap
+ sci-biology/repeatmasker-libraries
sci-biology/rmblast
>=sci-biology/trf-4.0.4
- sci-biology/repeatmasker-libraries
- sci-biology/phrap
- dev-perl/Text-Soundex"
+"
S="${WORKDIR}/RepeatMasker"
@@ -45,7 +46,7 @@ src_configure() {
# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
echo "
env
-${S}
+\"${S}\"
/opt/bin
1
/usr/bin
@@ -96,8 +97,8 @@ pkg_postinst(){
einfo "PATHs to the search binaries are defined in"
einfo "/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
einfo "Supported search engines are:"
- einfo "cross_match from sci-biology/phrap"
- einfo "rmblast from sci-biology/rmblast"
- einfo "nhmmer from >=sci-biology/hmmer-3.1"
+ optfeature "cross_match" sci-biology/phrap
+ optfeature "rmblast" sci-biology/rmblast
+ optfeature "nhmmer" >=sci-biology/hmmer-3.1
einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
}
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 16:47 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 16:47 UTC (permalink / raw
To: gentoo-commits
commit: 65eefd235ea15691fa4e51da736a624267e66fb6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 16:47:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 16:47:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=65eefd23
sci-biology/repeatmasker: depend on the now renamed package
Make users uninstall the previously installed files under the
sci-biology/trf package name.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 3da4241..f2a525a 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -23,7 +23,8 @@ RDEPEND="
sci-biology/phrap
sci-biology/repeatmasker-libraries
sci-biology/rmblast
- >=sci-biology/trf-4.0.4
+ !sci-biology/trf
+ >=sci-biology/trf-bin-4.0.4
"
S="${WORKDIR}/RepeatMasker"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 17:09 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 17:09 UTC (permalink / raw
To: gentoo-commits
commit: 00c9388d1211eb53a424c12f6607ef70054c6c8d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 17:09:12 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 17:09:12 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=00c9388d
sci-biology/repeatmasker: add missing call to default in src_prepare()
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index f2a525a..e0ad294 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -31,6 +31,7 @@ S="${WORKDIR}/RepeatMasker"
src_prepare(){
epatch "${FILESDIR}"/"${P}"__configure.patch
+ default
}
src_configure() {
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 17:16 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 17:16 UTC (permalink / raw
To: gentoo-commits
commit: 2ad8d135f344e32e7f1627bb293b776b36db9b80
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 17:16:00 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 17:16:00 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ad8d135
sci-biology/repeatmasker: respect EPREFIX
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index e0ad294..221c562 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -49,20 +49,20 @@ src_configure() {
echo "
env
\"${S}\"
-/opt/bin
+"${EPREFIX}"/opt/bin
1
-/usr/bin
+"${EPREFIX}"/usr/bin
Y
2
-/usr/bin
+"${EPREFIX}"/usr/bin
Y
4
-/usr/bin
+"${EPREFIX}"/usr/bin
Y
5" | "${S}/configure" || die "configure failed"
- sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
- -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/Libraries/\1"|' \
- -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
+ sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
+ -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
+ -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
}
# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm'
@@ -97,7 +97,7 @@ pkg_postinst(){
einfo "from Dfam-1.0 database www.dfam.org"
einfo "You can configure which search search engine is to be used and"
einfo "PATHs to the search binaries are defined in"
- einfo "/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
+ einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
einfo "Supported search engines are:"
optfeature "cross_match" sci-biology/phrap
optfeature "rmblast" sci-biology/rmblast
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 17:19 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 17:19 UTC (permalink / raw
To: gentoo-commits
commit: 879388b2a1e70cef663bc5c98b07a75e0dee369b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 17:19:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 17:19:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=879388b2
sci-biology/repeatmasker: more EPREFIX fixes
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 221c562..0f3be21 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -40,11 +40,11 @@ src_configure() {
# -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
sed -i -e 's/system( "clear" );//' "${S}/configure" || die
- mkdir -p "${D}"/usr/share/repeatmasker/Libraries/ || die
+ mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die
#
# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
# item does not get installed
- echo ">blah\natgc" > "${D}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+ echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
echo "
env
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 17:32 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 17:32 UTC (permalink / raw
To: gentoo-commits
commit: 336e1c45921c3e2cc5bade0d90a40c8c46276d11
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 17:31:40 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 17:31:40 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=336e1c45
sci-biology/repeatmasker: fix hardcoded paths to respect EPREFIX
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 0f3be21..8155caa 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -4,7 +4,7 @@
EAPI=6
-inherit eutils
+inherit eutils perl-module
MY_PV=${PV//\./-}
@@ -35,6 +35,11 @@ src_prepare(){
}
src_configure() {
+ sed -e "s#/usr/bin/which#${EPREFIX}/usr/bin/which#g" -i "${S}"/configure || die
+ sed -e "s#/usr/bin/perl#${EPREFIX}/usr/bin/perl#g" -i "${S}"/configure || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}#g" -i "${S}"/configure || die
# The below is wrong as it causes:
# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
# -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 18:04 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 18:04 UTC (permalink / raw
To: gentoo-commits
commit: ca02fa6f25e71ab9956a8fd21a9fa1ae80e1ff49
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 18:04:26 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 18:04:26 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca02fa6f
sci-biology/repeatmasker: remove escaping backslashes so that the ebuild works again
Also drop the full paths from configure which otherwise needed EPREFIX mangling
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 8155caa..a3ebd5a 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -35,8 +35,8 @@ src_prepare(){
}
src_configure() {
- sed -e "s#/usr/bin/which#${EPREFIX}/usr/bin/which#g" -i "${S}"/configure || die
- sed -e "s#/usr/bin/perl#${EPREFIX}/usr/bin/perl#g" -i "${S}"/configure || die
+ sed -e "s#/usr/bin/which#which#g" -i "${S}"/configure || die
+ sed -e "s#/usr/bin/perl#perl#g" -i "${S}"/configure || die
perl_set_version
insinto ${VENDOR_LIB}
sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}#g" -i "${S}"/configure || die
@@ -53,18 +53,18 @@ src_configure() {
# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
echo "
env
-\"${S}\"
-"${EPREFIX}"/opt/bin
+${S}
+${EPREFIX}/opt/trf/bin
1
-"${EPREFIX}"/usr/bin
+${EPREFIX}/usr/bin
Y
2
-"${EPREFIX}"/usr/bin
+${EPREFIX}/usr/bin
Y
4
-"${EPREFIX}"/usr/bin
+${EPREFIX}/usr/bin
Y
-5" | "${S}/configure" || die "configure failed"
+5" | "${S}"/configure || die "configure failed"
sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
-e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
-e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-01-31 18:10 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2017-01-31 18:10 UTC (permalink / raw
To: gentoo-commits
commit: eb753d08b6406bc1f65a7323efe99c5e3f5cee67
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 18:10:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 18:10:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb753d08
sci-biology/repeatmasker: add trailing '/' after vendor_perl path
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index a3ebd5a..5cae4ae 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -39,7 +39,7 @@ src_configure() {
sed -e "s#/usr/bin/perl#perl#g" -i "${S}"/configure || die
perl_set_version
insinto ${VENDOR_LIB}
- sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}#g" -i "${S}"/configure || die
+ sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
# The below is wrong as it causes:
# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
# -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2017-11-18 19:49 Justin Lecher
0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2017-11-18 19:49 UTC (permalink / raw
To: gentoo-commits
commit: 84e26e49f19bac5e2df49477506d6f5797b063fe
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 18 19:36:31 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 18 19:49:19 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=84e26e49
sci-biology/repeatmasker: Fix repoman warnings
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
Package-Manager: Portage-2.3.14, Repoman-2.3.6
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 2a264584c..47b4cfc7f 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -28,14 +28,13 @@ RDEPEND="
S="${WORKDIR}/RepeatMasker"
-src_prepare(){
- epatch "${FILESDIR}"/"${P}"__configure.patch
- default
-}
+PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
src_configure() {
- sed -e "s#/usr/bin/which#which#g" -i "${S}"/configure || die
- sed -e "s#/usr/bin/perl#perl#g" -i "${S}"/configure || die
+ sed \
+ -e "s#/usr/bin/which#which#g" \
+ -e "s#/usr/bin/perl#perl#g" \
+ -i "${S}"/configure || die
perl_set_version
insinto ${VENDOR_LIB}
sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
@@ -76,7 +75,7 @@ src_install() {
exeinto /usr/share/${PN}
for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
doexe $i
- dosym /usr/share/${PN}/$i /usr/bin/$i
+ dosym ../share/${PN}/$i /usr/bin/$i
done
perl_set_version
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/
@ 2018-11-30 15:42 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2018-11-30 15:42 UTC (permalink / raw
To: gentoo-commits
commit: 3dbfa5e99c249519ae8f9f7711974cfdc43a928c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 30 15:42:13 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 30 15:42:13 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3dbfa5e9
sci-biology/repeatmasker: update dependency on last supported db version
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 47b4cfc7f..2ff6c8be6 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -20,7 +20,7 @@ DEPEND=">=dev-lang/perl-5.8"
RDEPEND="
dev-perl/Text-Soundex
sci-biology/phrap
- sci-biology/repeatmasker-libraries
+ <=sci-biology/repeatmasker-libraries-20160829
sci-biology/rmblast
!sci-biology/trf
>=sci-biology/trf-bin-4.0.4
@@ -106,4 +106,6 @@ pkg_postinst(){
optfeature "rmblast" sci-biology/rmblast
optfeature "nhmmer" >=sci-biology/hmmer-3.1
einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
+ einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last"
+ einfo "version compatible with <repeatmasker-4.0.7"
}
^ permalink raw reply related [flat|nested] 15+ messages in thread
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